Software Resources for Remediated Data

This page presents a selection of software tools that are compatible with the nomenclature that is used in PDB Version 3.0 (remediated) and PDB Version 3.1 (data released after August 1, 2007).

Visualization Software

Refinement Software

No changes in refinement software or associated libraries are required to produce files for PDB deposition. The wwPDB will convert deposited files to PDB V3 nomenclature during the deposition and annotation process.

A version of the Phenix structure determination package will be released shortly which fully supports the PDB V3 nomenclature.

A reference library of standard amino acids and nucleotide monomers using the PDB V3 nomenclature and containing standard geometries [1-2] is available.
1. Engh, R.A. & Huber, R. (2001). International Tables for Crystallography, Vol F. edited by M.G.Rossmann & E. Arnold, pp 382-392. Dordrecht: Kluwer Academic Publishers
2. Clowney et al. (Geometric Parameters in Nucleic Acids: Nitrogenous Bases. Lester Clowney, Shri C. Jain, A. R. Srinivasan, John Westbrook, Wilma K. Olson, and Helen M. Berman. (1996), J. Am. Chem. Soc., 118, 509-518.)

Validation Software

The MolProbity webserver for macromolecular structure validation and improvement now accepts coordinate files in either PDB V2.3 or V3.0 format, uses the latter for internal computations, and can provide conversion in either direction. r500.f is a program which reads PDB V3 format data files and produces V3 validation records based standard geometries described in [1-2]. This Fortran 77 program requires supporting the supporting libraries standard_geometry.cif and symop.lib.
A revision of wwPDB annotation procedures documentation will released in September 2007
A new version of the RCSB validation software will be released in September 2007.

Tools Providing Nomenclature Conversion

A fast 2-way PDB format converter (in Perl or Python) dubbed the Remediator, converts PDB V2.3 atom names (including hydrogens) to PDB V3.0 names using the wwPDB's component dictionary, parsed into a hash table for speed. Also converts DNA residue names from A,C,T,G,U,I to DA,DC,DT,DG,DU,DI. These changes affect any PDB record that begins with ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, or LINK. The program has the capacity to convert in both directions by using the appropriate flag, but converts to the new format by default.
A PDB V2.3 to PDB V3 nomenclature converter tool consisting of the Fortran 77 program checknames.f and the supporting library standard_geometry.cif.
A PDB V3 to PDB V2.3 nomenclature converter is available as a web service

Molecular Modeling Software

The molecular modeling and simulation program YASARA supports the new PDB V3 nomenclature as of version 7.6.19 released in June 2007.


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